I like how many people have suggested all these different things, but I also feel how the OP is overwhelmed with all these different suggestions. I'm still not sure if OP is understanding what's causing the shrill highs between the two power amps. Let's start from the beginning.
Matrix power amp is a solid state power amp which is supposed to be flat as possible, which it is. It doesn't color your sound. That means it doesn't cut highs and lets all the frequencies through from the source. Its job is to keep your signal as transparent as possible.
VHT power amp uses tubes and is NOT flat. It does color your sound. It has that "tube warmness", "tube roundness" or whatever you wanna call it. It's pushing some and cutting some of the high frequencies, which people sometimes refer as "warm" or "tube sound". You can think of it as an eq, which sometimes can be useful, but you also can't get rid of if you want to.
See the problem here? You either have to lower the treble on the amp or use an always on EQ matched to the VHT power amp inside your Axe FX. I wouldn't suggest the latter, because it will most probably introduce some problems.
If your amp sound is too bright to begin with, it will sound too bright when using the Matrix. You can get away with the VHT power amp, because it's cutting some of the shrill high frequencies. This can become a problem when feeding a direct sound to PA or FOH. You might be enjoying a "nice warm tube sound" for yourself, but at the same time be feeding an overly bright sound to FOH because the VHT is not coloring that one.
Here's a few suggestions:
- If you plan to use direct sound from Axe FX to PA or FOH, always tweak with FRFR and with gig volume. Fletcher Munson is a real thing with every setup.
- If you use cabinet emulation, try to find a few impulse responses that don't have those shrill highs. Look for a typical or certain cabinet impulse you might feel using, for e.g. 4x12 Marshall impulse for Marshall amps. Then scroll between the impulses, use your ears and stop when you have something you like.
- If you feel like all impulse responses have too much high end, use the high cut until you don't hear those nasty frequencies. 5-8k high cut is sometimes needed when using bright impulse responses.
- If you still have shrill highs, lower the treble and presence on your amp. You can also try raising the amp master volume. Most of the time you shouldn't have to go deeper than that.
- If you still have shrill highs, go back to finding a right impulse or just change the amp. There's plenty to choose from. You might've just used a bright amp with a bright impulse. Bright + bright = too bright.